Note
Click here to download the full example code
AFQ API#
An example using the AFQ API
import os.path as op
import matplotlib.pyplot as plt
import nibabel as nib
import plotly
import pandas as pd
from AFQ.api.group import GroupAFQ
import AFQ.data.fetch as afd
Get some example data#
Retrieves High angular resolution diffusion imaging (HARDI) dataset from Stanford’s Vista Lab
see https://purl.stanford.edu/ng782rw8378 for details on dataset.
The data for the first subject and first session are downloaded locally (by default into the users home directory) under:
.dipy/stanford_hardi/
Anatomical data (anat) and Diffusion-weighted imaging data (dwi) are
then extracted, formatted to be BIDS compliant, and placed in the AFQ
data directory (by default in the users home directory) under:
AFQ_data/stanford_hardi/
This data represents the required preprocessed diffusion data necessary for intializing the GroupAFQ object (which we will do next)
The clear_previous_afq is used to remove any previous runs of the afq object stored in the AFQ_data/stanford_hardi/ BIDS directory. Set it to false if you want to use the results of previous runs.
afd.organize_stanford_data(clear_previous_afq=True)
Initialize a GroupAFQ object:#
Creates a GroupAFQ object, that encapsulates tractometry. This object can be used to manage the entire AFQ pipeline, including:
Tractography
Registration
Segmentation
Cleaning
Profiling
Visualization
In this example we will load the subjects session data from the previous step using the default AFQ parameters.
Note
The first time intializing the GroupAFQ object will download necessary waypoint regions of interest (ROIs) templates into AFQ data directory:
Human corpus callosum templates:
AFQ_data/callosum_templates/see https://digital.lib.washington.edu/researchworks/handle/1773/34926
Tract probability maps:
AFQ_data/templates/see https://figshare.com/articles/Tract_probability_maps_for_automated_fiber_quantification/6270434 # noqa
These waypoints ROIs will used to identify the desired white matter tracts.
This will also create an output folder for the corresponding AFQ derivatives
in the AFQ data directory: AFQ_data/stanford_hardi/derivatives/afq/
To initialize this object we will pass in the path location to our BIDS compliant data.
Note
As noted above, the Stanford HARDI data contains anatomical and diffusion weighted imaging (dwi) data. In this example, we are interested in the vistasoft dwi. For our dataset the dmriprep is optional, but we have included it to make the initialization more explicit.
Note
We will also be using plotly to generate an interactive visualization. So we will specify plotly_no_gif as the visualization backend.
myafq = GroupAFQ(
bids_path=op.join(afd.afq_home, 'stanford_hardi'),
preproc_pipeline='vistasoft',
viz_backend_spec='plotly_no_gif')
/opt/hostedtoolcache/Python/3.8.16/x64/lib/python3.8/site-packages/bids/layout/validation.py:156: UserWarning:
The PipelineDescription field was superseded by GeneratedBy in BIDS 1.4.0. You can use ``pybids upgrade`` to update your derivative dataset.
Reading in DTI FA (Diffusion Tensor Imaging Fractional Anisotropy)#
The GroupAFQ object holds a table with file names to various data derivatives.
For example, the file where the FA computed from DTI is stored can be
retrieved by inspecting the dti_fa property. The measures are stored
in a series, and since we only have one subject and one session we will
access the first (and only) file name from the example data.
Note
The AFQ API computes quantities lazily. This means that DTI parameters are not computed until they are required. This means that the first line below is the one that requires time.
We will then use nibabel to load the deriviative file and retrieve the data array.
Visualize the result with Matplotlib#
At this point FA is an array, and we can use standard Python tools to visualize it or perform additional computations with it.
In this case we are going to take an axial slice halfway through the FA data array and plot using a sequential color map.
Note
The data array is structured as a xyz coordinate system.
(-0.5, 105.5, 80.5, -0.5)
Visualizing bundles and tract profiles:#
The pyAFQ API provides several ways to visualize bundles and profiles.
First, we will run a function that exports an html file that contains an interactive visualization of the bundles that are segmented.
Note
By default we resample a 100 points within a bundle, however to reduce processing time we will only resample 50 points.
Once it is done running, it should pop a browser window open and let you interact with the bundles.
Note
Running the code below triggers the full pipeline of operations leading to the computation of the tract profiles. Therefore, it takes a little while to run (about 40 minutes, typically).
Note
You can hide or show a bundle by clicking the legend, or select a single bundle by double clicking the legend. The interactive visualization will also all you to pan, zoom, and rotate.
bundle_html = myafq.export("all_bundles_figure")
plotly.io.show(bundle_html["01"][0])